Read Alignment
Variant Calling
Column
Overview
- GATK4 best practices
- Site level filtering:
- bi-allelic SNPs
- 95% truth sensitivity (VQSR)
- Genotype level filtering:
- DP: 4 - 77 (mean DP + 4*SD)
- GQ >= 20
- Else missing (./.)
Number of Variants
| variable | raw | site_filtered | gt_filtered |
|---|---|---|---|
| TOTAL_SNPS | 16,643,754.00 | 9,115,052.00 | 5,126,585.00 |
| NUM_IN_DB_SNP | 12,117,419.00 | 8,486,322.00 | 4,846,921.00 |
| NOVEL_SNPS | 4,526,335.00 | 628,730.00 | 279,664.00 |
| PCT_DBSNP | 0.73 | 0.93 | 0.95 |
| DBSNP_TITV | 1.94 | 2.07 | 2.30 |
| NOVEL_TITV | 1.07 | 1.53 | 1.82 |
| TOTAL_INDELS | 3,454,237.00 | 0.00 | 0.00 |
| TOTAL_MULTIALLELIC_SNPS | 856,605.00 | 0.00 | 0.00 |
Column
SNPs per sample
Sample metrics
Population metrics
Population VCFs were produced from cohort final-VCF by extracting samples and removing fixed reference sites (GT==“RR”) and all-missing sites (GT==“./.”).
Intersections (upsetr)
Missingness
| min_called_samples | DUK | DUC | DU6 | DU6P | DUhLB | FZTDU |
|---|---|---|---|---|---|---|
| 1 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| 2 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| 3 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| 4 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| 5 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| 6 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| 7 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| 8 | 1.00 | 0.99 | 0.99 | 1.00 | 1.00 | 1.00 |
| 9 | 1.00 | 0.99 | 0.99 | 0.99 | 1.00 | 1.00 |
| 10 | 0.99 | 0.99 | 0.99 | 0.99 | 0.99 | 1.00 |
| 11 | 0.96 | 0.99 | 0.84 | 0.99 | 0.97 | 1.00 |
| 12 | 0.92 | 0.98 | 0.66 | 0.98 | 0.95 | 0.99 |
| 13 | 0.88 | 0.95 | 0.50 | 0.96 | 0.91 | 0.99 |
| 14 | 0.83 | 0.91 | 0.38 | 0.93 | 0.86 | 0.97 |
| 15 | 0.78 | 0.86 | 0.27 | 0.89 | 0.82 | 0.94 |
| 16 | 0.73 | 0.79 | 0.19 | 0.85 | 0.76 | 0.90 |
| 17 | 0.67 | 0.70 | 0.13 | 0.80 | 0.71 | 0.85 |
| 18 | 0.61 | 0.60 | 0.08 | 0.74 | 0.65 | 0.79 |
| 19 | 0.54 | 0.49 | 0.05 | 0.67 | 0.59 | 0.72 |
| 20 | 0.46 | 0.38 | 0.03 | 0.58 | 0.52 | 0.65 |
| 21 | 0.38 | 0.26 | 0.01 | 0.47 | 0.45 | 0.57 |
| 22 | 0.29 | 0.16 | 0.01 | 0.34 | 0.37 | 0.50 |
| 23 | 0.20 | 0.08 | 0.00 | 0.21 | 0.28 | 0.40 |
| 24 | 0.11 | 0.03 | 0.00 | 0.09 | 0.18 | 0.29 |
| 25 | 0.03 | 0.01 | 0.00 | 0.03 | 0.08 | 0.14 |
Figures produced externally from site-filtered biSNPs with script “./batches123_04_FinalVCF/scripts/15_visualize_missingness.R”.
More about GT-filtering
| min_N_non_miss_per_group | N_SNPs |
|---|---|
| 10 | 8875347 |
| 11 | 7384239 |
| 12 | 5794507 |
| 13 | 4415506 |
| 14 | 3279141 |
| 15 | 2364751 |
| 16 | 1645183 |
| 17 | 1091424 |
| 18 | 683508 |
| 19 | 396131 |
| 20 | 206405 |
| 21 | 93424 |
| 22 | 34033 |
| 23 | 9207 |
| 24 | 1277 |
| 25 | 32 |
If 1/6 groups with min 20/25 non-miss samples: 7064770 SNPs
If 6/6 groups with min 20/25 non-miss samples: 34033 SNPs
SNP Annotations
LDD & SFS
Column
Allele frequency state per population
LD Decay
Column
Alternative Allele Frequency Distribution
Minor Allele Frequency Distribution
Diversity
Genetic Structure
Column
PC1 - PC2
PC2 - PC3
PC3 - PC4
PC4 - PC5
PC5 - PC6
Scree Plot
Column
Hierarchical Clustering
Admixture
Admixture detailed
Column
K2
K3
Column
K4
K5
Genetic Differentiation
Column
z-Fst Histogram
Column
z-Fst Boxplots
